Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate HSERO_RS19090 HSERO_RS19090 C4-dicarboxylate ABC transporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__HerbieS:HSERO_RS19090 Length = 431 Score = 284 bits (726), Expect = 4e-81 Identities = 173/418 (41%), Positives = 249/418 (59%), Gaps = 27/418 (6%) Query: 15 VIVAIAIGILLGH--FYPQTGVALKPLG-------DGFIKLIKMVIAPIIFCTVVSGIAG 65 + A+ +GIL+G+ F K L D F++LIKMVIAP++F T+V GIA Sbjct: 11 IFAAMLLGILVGYLIFSHNDKAQAKELAGYISIASDLFLRLIKMVIAPLVFSTLVVGIAH 70 Query: 66 MQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTA 125 M + KSVG+ G +L +F I S ++L +G+++ N++QPG G+ L + A A Sbjct: 71 MGDAKSVGRIFGKSLAWFFIASLVSLALGMIMANLLQPGAGV-----ALPSPDAAGAGLA 125 Query: 126 GKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAH 185 ++ F +++P +IV A A ++LQV++FS+ FG AL LG GK +L ID +H Sbjct: 126 TSKFTVKEFFNHLVPKSIVEAMAQNEVLQVVVFSMFFGIALASLGERGKHLLAVIDDLSH 185 Query: 186 VMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICR 245 M I +MK AP+ AMA T+ G+ LV M FY F LV+L I Sbjct: 186 TMLKITVYVMKFAPVAVFAAMAATVAVNGLEILVSFAVFMRDFY-----FSLVLLWVILI 240 Query: 246 AHGFSVLK-----LIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGY 300 A GF LK L+ I+E L+ T+SSE+A P++L ++R G K+ + V+P GY Sbjct: 241 AVGFIFLKKRIFHLLALIKEAFLLAFATASSEAAYPKLLDALDRFGVKRKISSFVMPMGY 300 Query: 301 SFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATL 360 SFNLDG+ IY T A +FIAQA HM I+ QIT++LVL+L+SKG AGV + +V+AATL Sbjct: 301 SFNLDGSMIYCTFATLFIAQAYGIHMPISTQITMMLVLMLTSKGIAGVPRASLVVIAATL 360 Query: 361 SAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKEL--DEDQLQAEL 416 ++P AGL +ILGID F+ R+ TN VGN++A+ VVAKW L +E+ +AE+ Sbjct: 361 HQF-NIPEAGLLVILGIDTFLDMGRSATNAVGNSIASAVVAKWEGGLMTEEEAARAEV 417 Lambda K H 0.326 0.142 0.402 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 450 Number of extensions: 23 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 444 Length of database: 431 Length adjustment: 32 Effective length of query: 412 Effective length of database: 399 Effective search space: 164388 Effective search space used: 164388 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory